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Series GSE35109 Query DataSets for GSE35109
Status Public on Jan 16, 2012
Title Genome-Wide Mapping Of Time-Series ChIP-Seq Data For Human ERα Breast Cancer Cell Line (MCF-7)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report the genome-wide mapping of time-series ChIP-seq data sets of human breast cancer ERα cell line (MCF-7). The 4 time points cover the 0, 1, 4 and 24 hours, respectively.
MCF-7 cells were maintained in a hormone-free medium (phenol red–free MEM with 2 mmol/L L-glutamine, 0.1 mmol/L nonessential amino acids, 50 units/mL penicillin, 50 Ag/mL streptomycin, 6 ng/mL insulin, and 10% charcoal-stripped FBS) for three days. MCF-7 cells were treated with DMSO at the 0 hour time point, and E2 (108 mol/L) at the 1, 4 and 24 hours. 5 x 107 cells were cross-linked with 1% formaldehyde for 10 min, at which point 0.125 M glycine was used to stop the cross-linking.
In brief, after crosslinking, cells were treated by lysis buffers and sonicated to fragment the chromatin to a size range of 500-1000 bps. Chromatin fragments were then immunoprecipitated with 10ug of antibody/magnetic beads. The antibodies against ERα were purchased from Santa Cruz Biotechnology (Santa Cruz, sc-8005 X).
After immunoprecipitation, washing and elution, ChIP DNA was purified by phenol:chloroform:isoamyl alcohol and solubilized in 70 μl of water.
The ChIP DNA sample was run in 12% PAGE and the 100-300 bps DNA fraction was excised and eluted from the gel slice overnight at 4°C in 300 μl of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate) and was purified using a QIAquick purification kit (Qiagen, cat#:28104).
The library was constructed using Illumina genomic DNA prep kit by following its protocol (Illumina, cat#:FC-102-1002), clusters were generated on the Illumina cluster station (Illumina, cat#:FC-103-1002), DNA samples (20 nM per sample) quantified by an Agilent Bioanalyzer, were loaded onto Illumina Genome Analyzer IIx (GAIIx) for sequencing according to the manufacturer's protocol.
Reads generated from the Illumina GAIIx pipeline were aligned to the Human Genome Assembly (NCBI build 36.1/hg18) using the ELAND algorithm.
Overall design E2-treated experiments on human breast cancer ERα cell line (MCF-7) across the 4 time points.
Contributor(s) Tang B, Jin VX
Citation(s) 23166858, 27690208
Submission date Jan 14, 2012
Last update date Oct 24, 2019
Contact name Binhua Tang
Organization name Harvard Medical School
Department BMI
Street address 10 Shattuck Street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (4)
GSM862178 ERα ChIP-seq 1
GSM862179 ERα ChIP-seq 2
GSM862180 ERα ChIP-seq 3
SRA SRP010341
BioProject PRJNA150903

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Supplementary file Size Download File type/resource
GSE35109_RAW.tar 341.9 Mb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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